/[MITgcm]/manual/manual_todo.txt

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-revision 1.5 by edhill,
Thu Apr  6 19:06:45 2006 UTC
+revision 1.10 by cnh,
Thu Apr  6 20:03:45 2006 UTC
 Line 3 
 Rebuild and set to do cron build - DONE
  To do
    - where to put under development links?
+     JMC would like to have some mention of unfinished things (checked in
+      but not that tested e.g. AB3)
+     Add an "Under development, chapter" - shortish description of what
+     is available (last chapter)
+ o HTML, scripts and front content
+   - pick a URL
+     TBD
    - mitgcm.org very front page.
      o too many clicks to get to model manual.
-Line 19 
 To do
+Line 29 
 To do
        Overview
        Tutorials (broken)
        Browse Code
+     o mitgcm.org (front content) [DONE]
        Get Code (where does this go to?)
+       get rid of * CVS current bullet
+       make HTML-enabled CVS code browser leap to MITgcm/MITgcm
      o authors
        John, Alistair, Jean-Michel, Patrick, Andrea, Steph, Helen,
        Martin, Baylor, Dimitris, David, Ed, Mick, Chris, Constantinos,
        Gael - others?
-     o Tutorials side bar link is broken
+     o words on http://mitgcm.org/r2_web_testing/latest
+       change to
-     o words
+        "access on-line Auser manual/A and Atable of contents/A
-       change to "access on-line Auser manual/A and Atable of contents/A
+         and browse the Aoverview section/A"
-       and browse the Aoverview section/A"
      o finite-volume doesn't leap to FV figure
-     o the src and equation links don't come through to
+     o have another go at pnmcrop et al.
-       the html when they are in figures - see chapter 2 for some
-       examples.
-     o degree symbols keep getting "dropped down" - problem with
-       pnmcrop et al.
+     o Need an empty package as part of distribution. Check out atm_common
- Contents
+ o Latex
-     Intro                  - CNH
+     Chapter 1                 - CNH
        o single kernel diagram -
            add reference to MWR paper
-Line 109 
 Contents
+Line 118 
 Contents
        o Kinematic boundary conditions
-       o Hydrostatic, Quasi-hydrostatic, Quasi-nonhydrostatic and Non-hydrostatic forms
+       o Hydrostatic, Quasi-hydrostatic, Quasi-nonhydrostatic and
-         need to tidy up discussion of shallow-atmosphere to be
+         Non-hydrostatic forms
-         consistent with the code or change code to be consistent
+          need to tidy up discussion of shallow-atmosphere to be
-         with the discussion!
+          consistent with the code or change code to be consistent
-         make references hyperlinks
+          with the discussion!
-         add stuff too
+          make references hyperlinks
+          add stuff too
+          JMC remove QNH atmosphere
+          need to sort out calc_gw for deep atmosphere
        o Finding the pressure field
-         make references hyperlinks
+          make references hyperlinks
-         add forward references to manual algorithm section
+          add forward references to manual algorithm section
-         change Elliptic to "elliptic"
+          change Elliptic to "elliptic"
        o Forcing and dissipation
-         make "physics packages" refer to chapter 6.
+          make "physics packages" refer to chapter 6.
-         should we move "external forcing" et. al to a
+          should we move "external forcing" et. al to a
-         generic_forcing_driver package?
+          generic_forcing_driver package?
          viscosities
-         update to mention Smag/Leith (Ah and A4 not constant)
+          update to mention Smag/Leith (Ah and A4 not constant)
-         and to have forward references to numerical section
+          and to have forward references to numerical section
-         tracers
+          tracers
-         forward references to numerical section, reddy, GM etc...
+          forward references to numerical section, reddy, GM etc...
-         add references to literature
+          add references to literature
        o 1.3.8 Vector invariant form
          forward references to numerical section
-Line 157 
 Contents
+Line 169 
 Contents
          PH to do something
-     Discretization and alg - JMC+CNH
+     Change hydrodynamical to "dynamical"
-     Tutorials              - AM
+     Examples
-.1 "Where to find"
-        o link to Pelican not needed
-        o mailman twice (why?)
-        o no htdig (gone? - I liked it)
-      intro part
+         - extra "in action" cases
-      individual experiments
-      offline - duplicate inputs, what is it, tidy up cfc v.
+           o high res ocean with diurnal atmospheric state forcing
-                other offline.
+             - links to ingrid output
+               CNH/Dimitris
-     Software               - EH to review
+           o realistic FIZHI from Andrea
+             - links to ingrid output
+               from AM
-     some to be done on resource estimates at the end - needs sorting.
+           o with seaice on high res cube
+             - links to ingrid output
+               CNH/Dimitris
-     Automatic Diff         - CE
+           o coupled aqua, ridge world etc...
+             - links to ingrid output
+               get stuff from Daniel
-     Physical Packages      - ???
+           o constrained lab simulation
+             - links to ingrid output for model and lab
+               fields
+               get stuff from Sai/Andrew
-     Diags and tools        - ???
+           o sensitivity wrt to iron
-     Interface with ECCO    - ???
+           o optimization
+             - update to link to latest ECCO sites and GF
+               related material
-     Model uses             - ???
+           o eddy diffusivity transport application
-     Building document      - ???
+           o Gas giant?
-     via cron
-     tweaking latex2html etc..
-     Src Code tree (rename
-     examples etc..)        - ???
- Documentation
+ >>>> from JM
-. Introduction
-. Discretization and Algorithm
+ manual, section.2 :
-.13.5 Lateral dissipation
+ In general:
-     o need to relate c11, c12 etc.. to COSFAC, USE_COS etc... flags
+ - add more refences/links to S/R & variable name
-       in code need to explain why cos()3/2 turns out to be
+ - would be nice to have an active link to the fortran-file
-       scaling (not cos()2)
+   for all the S/R & eq.Number in the "calling-tree" boxes
+ - search for CALC_MOM_RHS and replace it by the appropriate S/R
+   (mom_flux_form, mom_vecinv, dynamics)
+ - Problem with notation: in section.1 \vec{\bf v_h} (or \vec{\mathbf{v}}_{h})
+ was used for the horizontal velocity vector, and the 3.D vector was \vec{\mathbf{v}}
+ in section.2, \vec{\bf v} is used instead and 3.D velocity vector is
+ simply written \vec{v}.
+ I would suggest to keep the notation as they are (since they are consistent
+ inside each section) but may be to move the "notation.tex" piece
+ at the beginning of section.2 and to mention clearly the changes between
+ the 2 sections.
-.13.6 Vertical dissipation
+ in content: Horizontal Dissipation: 2 times in vector-invariant section
-     o update to have reference to Baylors section
-       reference to implicit discussion in time-stepping part of manual
+.1 time-stepping (part2/time_stepping.tex)
+ - this is not clear to me:
-. Tutorials
+ >> In all the above configurations it is also possible to substitute the
-    reorg'd into
+ >> Adams-Bashforth with an alternative time-stepping scheme for terms
-    intro part
+ >> evaluated explicitly in time
-    individual experiments
-. Software Architecture
-. Automatic Differentiation
+.2 rigid-lid:
-. Physical Parameterization and Packages
+ - At some point, would be better to replace "g \eta" with "\Phi_s (cg2d_x)"
+   to stay closer to the code.
+ - mention section 2.5 implicit-Time-stepping (for vertical viscosity)
-. Diagnostics and tools
+.3 linear free-surface:
+ - add ref(+link) to S/R names:
+ - add ref(+link) to Crank-Nickelson section 2.9.1
-. Interface with ECCO
+.4 Adams-Bashforth
+ - add stability diagrams (I have some figures that I can put)
+ - add link for var. forcing_In_AB
+ - add S/R link for S/R ADAMS_BASHFORTH2
-. Model uses
+.5 Implicit time-stepping
-    Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...
+ - add name of S/R: IMPLDIFF, GAD_IMPLICIT_R, MOM_U_IMPLICIT_R
-    (check in support for more names)
+         SOLVE_TRIDIAGONAL, SOLVE_PENTADIAGONAL
+ - update: also used for vertical advection
-  Need an empty package as part of distribution
+.6 Synchronous time-stepping:
+ - add link for S/R THERMODYNAMICS, DYNAMCIS, SOLVE_FOR_PRESSURE,
+                    MOMENTUM_CORRECTION_STEP.
-  latex2html equation formatting is still a bit weird in places. Need to have another go if we have a chance - especially the degree symbol seems to jump around somewhat!
+.7 Stagger baroclinic time-stepping
+ - mention AB(T,S) instead of AB(Gt,Gs) (in development) at the end
- Chapter 1
+.8 NH
+ - add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D
-     Change hydrodynamical to "dynamical"
+.9 Variants on Free-Surface
+ - Delta.t mis-written (eq.2.73)
+ - Eq.Num missing (has been fixed since)
+ - u* is stored in gU (and not in gUnm1)
+ - Phi_nh in NH_VARS.h
+ - add link to S/R file: SOLVE_FOR_PRESSURE, CALC_DIV_GHAT, CG2D, CG3D,
+   INI_CG2D, INI_CG3D
-     Examples
+.9.1 Crank-Nickelson
+ - link for variable: implicSurfPress, implicDiv2DFlow, useRealFreshWater
+.9.2 NLFS
+ - eq.Nb are wrong in html
+ - 2.9.2.4 : set of eq. appears wrong in html (but right in .dvi)
-         - extra "in action" cases
+.10.1 Notation
+ - Area definition is not really used like this
-           o high res ocean with diurnal atmospheric state forcing
+ >> Ao : Area of the face orthogonal to "o" direction (o=u,v,w)
-             - links to ingrid output
-               CNH/Dimitris
-           o realistic FIZHI from Andrea
+   Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to
-             - links to ingrid output
+   the model variables) are used (e.g., see section 2.10.5)
-               from AM
-           o with seaice on high res cube
+.10.5 Horizontal grid:
-             - links to ingrid output
+ - fig.2.8 : should use Aw,As consistently in this figure description,
-               CNH/Dimitris
+   in the figure itself, as it is in the text.
+ - curvilinear:
+   to add: mention the angle of the grid direction relative to
+   Eastward, Northward direction.
+   + mention horizGridFile= in file "data" (PARM04)
+ - add cylindrical grid description
+    need to do a better job of relating model variables to this diagram
-           o coupled aqua, ridge world etc...
-             - links to ingrid output
-               get stuff from Daniel
-           o constrained lab simulation
+.11 Continuity & Horizontal Pressure gradient terms
-             - links to ingrid output for model and lab
+  - mention that d.Phi/dr|s =g if using z coordinate
-               fields
+  - eq. 2.90 not clear regarding \delta_k(P-E)
-               get stuff from Sai/Andrew
+  better to add the free surface eq: d.eta/dt = w_s + P-E
-           o sensitivity wrt to iron
+.12 Hydrostatic balance
+  - add ref to Atmosphere Appendix section (1.4) since Adcroft 2002
+    is hard to find
+  - add ref to section 1.3.4 (Hydrostatic, Quasi-Hydrostatic & Non-H)
+     and in section 1.3.4: remove the 1.3.4.3.2 subsection:
+                        Quasi-nonhydrostatic Atmosphere
-           o optimization
+.13.2 Coriolis terms
-             - update to link to latest ECCO sites and GF
+  - note: the discretization used when useEnergyConservingCoriolis=T
-               related material
+    has no hFac and no Area and is still different from the form
+    described here (with Area & hFac);
-           o eddy diffusivity transport application
+.13.5 Lateral dissipation
+  - add description of how to use cosFactor & cosPower
+  - add the parameter correspondence: Ah <-> viscAh ; A4 <-> viscA4
+     o need to relate c11, c12 etc.. to COSFAC, USE_COS etc... flags
+       in code need to explain why cos()3/2 turns out to be
+       scaling (not cos()2)
-           o Gas giant?
+.13.6 Vertical dissipation
+  - mention the implicit vertical viscosity option and ref to section 2.5
+  - add the parameter correspondence: Av <-> viscAr (and might change also
+    the notation to Ar)
- Chapter 6
+.14 Vector invariant momentum equations
+  - indicate that the NH pieces (vertical momentum eq) are not yet coded
+    and that the NH code uses the flux form.
-    the master package diagram does not appear in the document
+.14.6 Horizontal dissipation -> Horizontal Divergence
-    pkg/ptracers doesn't seem to have any documentation (see packages list below)
+.14.7 Horizontal dissipation
+  - add the parameter correspondence: A_D,A_z <-> viscAhD,viscAhZ
+    and A_D4,A_z4 <-> viscA4D,viscA4Z
+.16 & 2.17 & 2.18 :
+  - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options
+.20.2 mercator, non-dimensional Equations:
+ - does not use std notation
+ - would be better as an appendix of section 2.20:
+ (e.g changing the tile to:
+  Appendix: non-dimensional Equations on Spherical-Polar grid.)
-.10.5 Horizontal grid
+ JM
-    need to do a better job of relating model variables to this diagram
+ >>>> From Ed
+ Here are the remaining bits for Chap 4 :
- Master list of packages
+  - The grammar/flow could still use some work.  Boo was an English
+    major and has experience editing/proofing technical papers.  I
+    could print out a copy and ask her to read it and suggest
+    improvements.
+  - missing references (if you point me towards URLs, I'll add them
+    to the bibliography):
+      \ref{ref hoe and hill, ecmwf}
+      \ref{magicgarden}
+      \ref{IBMLAPI}
+      \ref{Memorychannel}
+      \ref{hoe-hill:99}
+  - There are a few empty sub-sections at the end of Chap 4 that
+    should either be commented out or fleshed out.
+ and thats about it for Chap 4.
+ Add more to quick links on front page
+ Chapter 6
+    the master package diagram does not appear in the document
+    pkg/ptracers doesn't seem to have any documentation (see packages list below)
+ Master list of packages (add this to beginning of chap 6)
  admtlm/               - autodiff (chapter 5)
- aim/                  - 6.4.1 (content needs fixing - JM to do)
+ aim/                  - retired
  aim_compon_interf/    - 6.6 (no content yet)
  aim_ocn_coupler/      - 6.6 (no content yet)
- aim_v23/              - retired
+ aim_v23/              - 6.4.1 (content needs fixing - JM to do)
  atm_common/           - 6.6 (no content yet)
  autodiff/             - autodiff (chapter 5)
  bulk_force/           - 6.3.3
-Line 357 
 Need to get packages to contain their av
+Line 457 
 Need to get packages to contain their av
  Figure 6.8 is missing
+.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997
- >>>> From Ed
+  Figure 6.8 is missing
- Here are the remaining bits for Chap 4 :
-  - The grammar/flow could still use some work.  Boo was an English
-    major and has experience editing/proofing technical papers.  I
-    could print out a copy and ask her to read it and suggest
-    improvements.
-  - missing references (if you point me towards URLs, I'll add them
-    to the bibliography):
-      \ref{ref hoe and hill, ecmwf}
-      \ref{magicgarden}
-      \ref{IBMLAPI}
-      \ref{Memorychannel}
-      \ref{hoe-hill:99}
-  - There are a few empty sub-sections at the end of Chap 4 that
-    should either be commented out or fleshed out.
- and thats about it for Chap 4.
- Add more to quick links on front page
  >>>> From Andrea
-Line 490 
 the verification directory
+Line 567 
 the verification directory
 .20.1 - link to doc at end of section points to this section
 .20.2 - link to doc at end of section points to this section
- >>>> from JM
+      offline - duplicate inputs, what is it, tidy up cfc v.
+                other offline. JM thinks these need tidying up.
- manual, section.2 :
- In general:
- - add more refences/links to S/R & variable name
- - would be nice to have an active link to the fortran-file
-   for all the S/R & eq.Number in the "calling-tree" boxes
- - search for CALC_MOM_RHS and replace it by the appropriate S/R
-   (mom_flux_form, mom_vecinv, dynamics)
- - Problem with notation: in section.1 \vec{\bf v_h} (or \vec{\mathbf{v}}_{h})
- was used for the horizontal velocity vector, and the 3.D vector was \vec{\mathbf{v}}
- in section.2, \vec{\bf v} is used instead and 3.D velocity vector is
- simply written \vec{v}.
- I would suggest to keep the notation as they are (since they are consistent
- inside each section) but may be to move the "notation.tex" piece
- at the beginning of section.2 and to mention clearly the changes between
- the 2 sections.
- in content: Horizontal Dissipation: 2 times in vector-invariant section
-.1 time-stepping (part2/time_stepping.tex)
- - this is not clear to me:
- >> In all the above configurations it is also possible to substitute the
- >> Adams-Bashforth with an alternative time-stepping scheme for terms
- >> evaluated explicitly in time
-.2 rigid-lid:
- - At some point, would be better to replace "g \eta" with "\Phi_s (cg2d_x)"
-   to stay closer to the code.
- - mention section 2.5 implicit-Time-stepping (for vertical viscosity)
-.3 linear free-surface:
- - add ref(+link) to S/R names:
- - add ref(+link) to Crank-Nickelson section 2.9.1
-.4 Adams-Bashforth
- - add stability diagrams (I have some figures that I can put)
- - add link for var. forcing_In_AB
- - add S/R link for S/R ADAMS_BASHFORTH2
-.5 Implicit time-stepping
- - add name of S/R: IMPLDIFF, GAD_IMPLICIT_R, MOM_U_IMPLICIT_R
-         SOLVE_TRIDIAGONAL, SOLVE_PENTADIAGONAL
- - update: also used for vertical advection
-.6 Synchronous time-stepping:
- - add link for S/R THERMODYNAMICS, DYNAMCIS, SOLVE_FOR_PRESSURE,
-                    MOMENTUM_CORRECTION_STEP.
-.7 Stagger baroclinic time-stepping
- - mention AB(T,S) instead of AB(Gt,Gs) (in development) at the end
-.8 NH
- - add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D
-.9 Variants on Free-Surface
- - Delta.t mis-written (eq.2.73)
- - Eq.Num missing (has been fixed since)
- - u* is stored in gU (and not in gUnm1)
- - Phi_nh in NH_VARS.h
- - add link to S/R file: SOLVE_FOR_PRESSURE, CALC_DIV_GHAT, CG2D, CG3D,
-   INI_CG2D, INI_CG3D
-.9.1 Crank-Nickelson
- - link for variable: implicSurfPress, implicDiv2DFlow, useRealFreshWater
-.9.2 NLFS
- - eq.Nb are wrong in html
- - 2.9.2.4 : set of eq. appears wrong in html (but right in .dvi)
-.10.1 Notation
- - Area definition is not really used like this
- >> Ao : Area of the face orthogonal to "o" direction (o=u,v,w)
-   Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to
-   the model variables) are used (e.g., see section 2.10.5)
-.10.5 Horizontal grid:
- - fig.2.8 : should use Aw,As consistently in this figure description,
-   in the figure itself, as it is in the text.
- - curvilinear:
-   to add: mention the angle of the grid direction relative to
-   Eastward, Northward direction.
-   + mention horizGridFile= in file "data" (PARM04)
- - add cylindrical grid description
-.11 Continuity & Horizontal Pressure gradient terms
-  - mention that d.Phi/dr|s =g if using z coordinate
-  - eq. 2.90 not clear regarding \delta_k(P-E)
-  better to add the free surface eq: d.eta/dt = w_s + P-E
-.12 Hydrostatic balance
-  - add ref to Atmosphere Appendix section (1.4) since Adcroft 2002
-    is hard to find
-  - add ref to section 1.3.4 (Hydrostatic, Quasi-Hydrostatic & Non-H)
-     and in section 1.3.4: remove the 1.3.4.3.2 subsection:
-                        Quasi-nonhydrostatic Atmosphere
-.13.2 Coriolis terms
-  - note: the discretization used when useEnergyConservingCoriolis=T
-    has no hFac and no Area and is still different from the form
-    described here (with Area & hFac);
-.13.5 Lateral dissipation
-  - add description of how to use cosFactor & cosPower
-  - add the parameter correspondence: Ah <-> viscAh ; A4 <-> viscA4
-.13.6 Vertical dissipation
-  - mention the implicit vertical viscosity option and ref to section 2.5
-  - add the parameter correspondence: Av <-> viscAr (and might change also
-    the notation to Ar)
-.14 Vector invariant momentum equations
-  - indicate that the NH pieces (vertical momentum eq) are not yet coded
-    and that the NH code uses the flux form.
-.14.6 Horizontal dissipation -> Horizontal Divergence
-.14.7 Horizontal dissipation
-  - add the parameter correspondence: A_D,A_z <-> viscAhD,viscAhZ
-    and A_D4,A_z4 <-> viscA4D,viscA4Z
-.16 & 2.17 & 2.18 :
-  - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options
-.20.2 mercator, non-dimensional Equations:
- - does not use std notation
- - would be better as an appendix of section 2.20:
- (e.g changing the tile to:
-  Appendix: non-dimensional Equations on Spherical-Polar grid.)
- JM
+. Model uses
+    Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...
+    (check in support for more names)

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